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- PDB-4oxm: CRYSTAL STRUCTURE OF Central Coiled-Coil from Influenza Hemagglut... -

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Basic information

Entry
Database: PDB / ID: 4oxm
TitleCRYSTAL STRUCTURE OF Central Coiled-Coil from Influenza Hemagglutinin HA2 without Heptad Repeat Stutter
ComponentsHA2-Del
KeywordsVIRAL PROTEIN / coiled-coil / Influenza / Hemagglutinin / Stutter
Function / homologyHaemagglutinin, influenzavirus B / Haemagglutinin / Haemagglutinin, influenzavirus A/B / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / viral envelope / Truncated hemagglutinin
Function and homology information
Biological speciesunidentified influenza virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsMalashkevich, V.N. / Higgins, C.D. / Lai, J.R. / Almo, S.C.
CitationJournal: to be published
Title: CRYSTAL STRUCTURE OF Central Coiled-Coil from InfluenzaHemagglutinin HA2 without Heptad Repeat Stutter
Authors: Malashkevich, V.N. / Higgins, C.D. / Lai, J.R. / Almo, S.C.
History
DepositionFeb 5, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 30, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Database references
Revision 1.2Nov 22, 2017Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: citation / pdbx_database_status ...citation / pdbx_database_status / pdbx_entity_src_syn / pdbx_struct_assembly / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _pdbx_database_status.pdb_format_compatible ..._citation.journal_id_CSD / _pdbx_database_status.pdb_format_compatible / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.4Mar 27, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HA2-Del
B: HA2-Del
C: HA2-Del


Theoretical massNumber of molelcules
Total (without water)13,8253
Polymers13,8253
Non-polymers00
Water1,26170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4940 Å2
ΔGint-35 kcal/mol
Surface area7480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.424, 58.424, 66.994
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-113-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYLYSLYSAA43 - 823 - 38
21GLYGLYLYSLYSBB43 - 823 - 38
12TRPTRPTYRTYRAA42 - 832 - 39
22TRPTRPTYRTYRCC42 - 832 - 39
13GLYGLYLYSLYSBB43 - 823 - 38
23GLYGLYLYSLYSCC43 - 823 - 38

NCS ensembles :
ID
1
2
3

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Components

#1: Protein/peptide HA2-Del


Mass: 4608.172 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: peptide synthesis / Source: (synth.) unidentified influenza virus / References: UniProt: A8TXX2*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 46.15 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M Li-sulfate, 0.1M sodium-cacodylate:HCl, pH 6.5, 30% PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9791 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Aug 14, 2012
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 10677 / % possible obs: 98.3 % / Redundancy: 10.3 % / Rmerge(I) obs: 0.075 / Χ2: 1.134 / Net I/av σ(I): 25 / Net I/σ(I): 14.2 / Num. measured all: 109811
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.9-1.9310.30.6295471.179100
1.93-1.9711.10.5115121.281100
1.97-2.0111.70.4245441.232100
2.01-2.0511.50.325261.287100
2.05-2.0911.70.2675381.272100
2.09-2.1411.50.2265161.3100
2.14-2.1911.50.195331.219100
2.19-2.2511.30.1655551.214100
2.25-2.3211.30.155371.172100
2.32-2.3911.10.1275271.033100
2.39-2.48110.1185521.168100
2.48-2.5810.90.0995181.054100
2.58-2.710.70.0945501.114100
2.7-2.8410.40.0845231.0399.6
2.84-3.0210.10.0735500.92399.1
3.02-3.259.40.0675410.92597.8
3.25-3.588.20.0615311.01396.7
3.58-4.097.30.0565390.91296.8
4.09-5.167.60.0545340.97296
5.16-5070.0575041.10682.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIXphasing
REFMAC5.8.0049refinement
PDB_EXTRACT3.14data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: UNPUBLISHED STRUCTURE

Resolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.917 / SU B: 8.276 / SU ML: 0.124 / Cross valid method: THROUGHOUT / ESU R: 0.171 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27156 511 4.8 %RANDOM
Rwork0.21106 ---
obs0.21382 10144 98.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.856 Å2
Baniso -1Baniso -2Baniso -3
1--1.38 Å2-0.69 Å20 Å2
2---1.38 Å20 Å2
3---4.48 Å2
Refinement stepCycle: final / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms964 0 0 70 1034
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.019981
X-RAY DIFFRACTIONr_bond_other_d0.0060.02956
X-RAY DIFFRACTIONr_angle_refined_deg1.2481.9491306
X-RAY DIFFRACTIONr_angle_other_deg1.51332202
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3465112
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.69625.59359
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.62215202
X-RAY DIFFRACTIONr_dihedral_angle_4_deg4.941156
X-RAY DIFFRACTIONr_chiral_restr0.0730.2133
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021115
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02233
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.5122.883453
X-RAY DIFFRACTIONr_mcbond_other3.5182.877452
X-RAY DIFFRACTIONr_mcangle_it4.0714.249559
X-RAY DIFFRACTIONr_mcangle_other4.0694.257560
X-RAY DIFFRACTIONr_scbond_it5.5813.647528
X-RAY DIFFRACTIONr_scbond_other5.5673.649528
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.1925.228746
X-RAY DIFFRACTIONr_long_range_B_refined9.96225.5151224
X-RAY DIFFRACTIONr_long_range_B_other9.96225.1931201
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A15890.2
12B15890.2
21A15500.24
22C15500.24
31B15200.22
32C15200.22
LS refinement shellResolution: 1.9→1.948 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 39 -
Rwork0.281 764 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.90266.11950.320112.93690.69890.0801-0.08140.0480.1073-0.15420.06130.2542-0.0371-0.0350.02010.0643-0.01070.00020.0720.00540.0641-1.06134.7848.768
211.151112.35962.182617.45383.30912.01110.01770.15260.1681-0.13640.04450.3228-0.1657-0.0477-0.06230.16060.0185-0.01670.1296-0.00370.02342.10535.9570.253
32.82866.16242.738116.78577.71544.5474-0.13540.2497-0.0635-0.01440.2917-0.28170.00380.2675-0.15630.051-0.0066-0.00390.10370.00840.0097.96131.8335.511
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A41 - 83
2X-RAY DIFFRACTION2B43 - 83
3X-RAY DIFFRACTION3C42 - 83

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